Protein

Again, as you read this lecture, you should consider how this information affects
you personally and how the person whose diet you tracked compares to this information...

Proteins are polymers of amino acids (AA's). A very
small protein, insulin, has 87 AA's in the polymer; a relatively large protein, one
of the smaller contractile proteins from the lower back muscles of a rabbit,
has 247 AA's in the polymer. Any polymer of amino acids can be called a polypeptide. I prefer to limit the term protein to those polypeptides which have Biological
significance, and will do so for the remainder of these lectures.

§ 1. Amino Acids (or “AA”) and protein structure

Amino acids are organic molecules, with 1 Carbon (C) atom, plus an amino group
(-NH2) and an acid group (our old friend, -(C=O)-OH). In the center
between the amino and the acid, we place our single Carbon atom (-C-) and call it the
central carbon [because it is roughly centered between the two radicals]. We usually
draw the amino on the left and the acid on the right:
H2N-(HC-)-COOH, or H2N-(HC-)-(C=O)-OH,
where the central -(HC-)- is meant to represent a C with an H on one side (up)
and an unused bond location on the other side (down). To the unused bond location we
attach a ‘side chain’ or radical (R):
H2N-(HCR)-COOH.
The side chain may be simple, branched, or even a ring structure containing
Carbon, Hydrogen, Oxygen, and sometimes Nitrogen or Sulfur. Of the many AA's known to
exist, only 20 are commonly found in proteins. The chemical structures [which differ
in their side chains (-R)] of these 20 AA's can be found in most A &amp P texts, or
intro Biology texts [if you care, or even if you don't really care].

&nbsp Amino acids are polymerized, as usual, by dehydration. One Hydrogen
(H) is removed from the amino group on the second AA, and the hydroxyl (OH) is
removed from the acid group on the first AA. The Nitrogen (N) of amino group is then
bonded to the Carbon (C) of the acid group [using
the -(NH)- to indicate that the other H is to the side]:
H-(NH)-(HCR)-(CO)-OH H-(NH)-(HCR)-(CO)-OH
H-(NH)-(HCR)-(CO)-(NH)-(HCR)-(CO)-OH
&nbsp + &nbsp H-OHThe N-C bond is called a peptide bond, because peptic
is the Greek term for the contents of the stomach (especially when the contents have
been rejected by the stomach). Before Biologists knew Chemistry, the enzyme which
digests protein in the stomach was named ‘peptic juice.’ When Biologists
started learning Chemistry, we changed the name of the enzyme to peptase, for
‘stomach enzyme,‘ and adopted the name peptide bond for the bond digested
by peptase. The polymer of AA's ought to be called a poly-amino acid, but we didn't
know chemistry very well, so improperly named the polymer a polypeptide. A dipetide
has 2 AA's, but only one peptide bond [Another example of ‘interesting’ trivia
which you are welcome to ignore at your pleasure]. A non-trivial tidbit [which you may
also ignore] is that the AA's in a polypeptide (or protein) are numbered from the
amino-end, and the polypeptides are assembled by ribosomes from the amino-end. I am
not sure whether they are digested from the acid-end, or a random locations
[although I suspect it is random]. The baby-friendly ‘proteins’ in some
baby formula and first ‘solid’ foods are actually proteins which have been
digested to shorter [and more easily digested] polypeptides. “Aged” protein
foods, such as tender beef and cheese also have pre-digested polypeptides, where mold
is used to do the digesting. When beef hangs in the locker plant [as in one of the
Rocky movies. The side of beef Rocky used as a punching bag would make very
tender, melt-in-your-mouth steaks because the muscles would have been further broken
down by the physical blows], it becomes fuzzy green. The fuzz is scraped off, and
some of the beef proteins have been digested to more easily digested polypeptides.
You can also ‘tenderize’ beef (or any red meat) by adding protein-digesting
enzymes from plants (such as Adolph's meat tenderizer or garlic) as a rub [which
works better if you repeatedly stab the meat with a fork as you apply the rub]. I
have no guess as to why plants need enzymes to digest cows. Likewise, milk solids can
be separated from the whole milk by adding vinegar (acetic acid solution) at less
than 1 cup per gallon of whole milk to make curds and whey [Little Miss Muffet's
favorite snack for eating on a “tuffet” (a cushioned stool)]. The curds
contain most of the protein and fats; and the whey is skim milk with most of the
lactose. The curds are separated from whey by filtering the mixture through cheese
cloth (with rather large holes between the threads), then wrapping the curds in the
cheese cloth and hanging it in a cold, dark place until it becomes fuzzy green. Most
of the fuzz is removed by peeling off the cheese cloth, exposing the cheese. The
cheese is then wrapped in wax to slow the growth of the mold (by restricting the air
supply). If you leave real cheese [not “American processed cheese”] in the
refrigerator too long, it again becomes fuzzy green. You can safely slice off the
fuzzy green parts and eat the now sharper cheese (but if the fuzz is any other color,
such as black, you should discard the spoiled cheese) . If you skip the molding
process, and rinse the curds, still in the cheese cloth, with water, you get cottage
cheese.
American process cheese (most pre-packaged cheese slices and cheese spreads [such as
Velvetta or CheeseWhiz]) will not grow mold very well, but will support bacterial
growth and accumulation of bacterial toxins. Spoiled proceesed cheese cannot be eaten
safely! You can also hire bacteria to pre-digest the curds, and make yogurt; but if
yogurt has been in the refrigerator too long [beyond the “best by” date on
the package], it may have become too toxic to eat safely.
&nbsp &nbsp The numbering of the AA's allows us to write down the
sequence of the AA's in a protein, which we want to do
because the sequence is extremely important to the function of the protein. Each
different protein has a unique sequence, even similar proteins from different
species. Beef insulin differs from Human insulin by substitution of 4 AA's at
non-critical locations, so beef insulin has been used successfully to treat Human
diabetes. Sheep insulin differs from Human insulin by 6 substitutions, two of which
are in critical locations, so sheep insulin does not work well in Human
diabetics. Because of the differences in proteins between species, each species has a
unique ratio of the 20 key AA's. The dietary intake of protein must duplicate the
correct Human ratio of AA's to provide maximum health to Humans. This also applies to
pet foods, so I am unsure how cereal [and even vegetables] added to cat food is
supposed to be good for a carnivorous cat. Fortunately, cats and dogs don't read
Nutrition textbooks, and don't realize that Human-like diets may not be healthy for
them -and they still manage to keep setting new records for longevity. A ‘typical’
[that is, a theoretical] Human requires about one serving of red meat per week to get
the correct ratio of amino acids in their diet. One serving was once-upon-a-time
called a ‘petite’ steak on restaurant menus, and is no larger than 6 oz; not
half a cow. Some friends of mine used to have ‘contests’ to see who could
eat the largest slab of roast beef tenderloin; all but one has now had their first
(or more) heart attack, and he is being treated to prevent the heart attack after his
first angina pectoris [sometimes called a “mini-heart attack”, which is
not accurate, and is mis-leading]. While they were working on their heart attacks, I
would order a white fish, eat half of it and take the other half home for a second
meal [a single serving according to the menu was a whole fish, although nutritionally
a single serving is one filet, or less for most white fish which tend to large
compared to a perch].

&nbsp &nbsp While semi-vegetarian cats are a puzzlement to me, even more
mysterious are vegetarian Humans. Anatomically and physiologically, Humans are
omnivores [this means a Human can, and should, eat anything that doesn't eat them
first (except for poisonous things, which sort of eat you after you eat them).
You have incisors for chopping vegetables (think rabbit, or even beaver, buck-teeth),
and canines (think “Lions and Tigers and Bears, oh my!”) for ripping the
flesh off Kentucky-fried chicken drumsticks. Your single stomach produces larger
amounts of peptase than do cows (with four stomachs for digesting grasses and weeds).
You have a moderate sized appendix, the same size (in volume not proportion of body
size) as vegee-eating laboratory white rats, for storing the bacteria that assist in
digesting fiber from lettuce. While you can eat anything that doesn't eat you first,
I do not recommend attempting to eat alligators in the wilds of Florida, nor the
sharks offshore from Florida, but there is a certain, almost evil, pleasure in eating
either one in restaurants in Asheville, North Carolina [the Asheville restaurants are
from personal experience, and I have encountered a few wild alligators in Florida but
I never met a shark without a thick glass wall between us]. True vegetarian and vegan
diets can not, in theory, provide the minimum dietary intake of all essential [see
Nutrition Now, 5th ed, table 15-2, pg. 15-4] AA's without also
providing more than the maximum tolerable dose of some AA's [see text pg. 15-9]. Again,
reality seems to contradict theory in that many religious and cultural groups have
managed to live for 100's of generations on vegetarian diets. What has not been
established with scientific rigor is that these groups function at optimal health.

§ 2. Protein function

Proteins come in two styles: structural proteins and enzymatic proteins. Most
dietary protein comes from structural proteins (in the food organisms), and is
digested to AA's and polypeptides. The amino acids are absorbed, but since storage of
amino acids is limited, most are used soon after being absorbed or are excreted.
Those AA's which are used perform only two [not four] major functions, and one minor
function.
&nbsp &nbsp Of the functions listed in Nutrition Now, 5th ed
(Table 15.1, pg. 15-3) numbers 1
&amp 3 are the same function: the AA's are used by ribosomes [mostly free ribosomes]
to synthesize structural proteins, either to build new tissues (number 1 in text) or
to replace damaged proteins in existing tissues (number 3 in text). The need for
replacement structural proteins is high simply because all chemical compounds
containing Nitrogen are unstable [perhaps the most unstable is trinitro-toulene,
commonly called TNT]. Each amino acid contains at least one Nitrogen (the one in the
amino group), and are thus unstable, with a tendency for the peptide bonds to break
spontaneously -yielding two polypeptides. The broken bonds cannot be repaired by any
known living creature, so the polypeptides are digested to AA's, while a replacement
molecule is being synthesized by free ribosomes at the location where the
‘old’ protein failed. Most of the AA's from the ‘old’ protein are
reclaimed for the next protein being assembled. This is why you can lose and replace
9 oz protein per day (text, pg. 15-3f [the “f” means “and following
page”, and “ff” would mean “and following pages”]),
yet absorb only about 2 to 3 oz protein per day.
&nbsp &nbsp The second function of proteins listed in the text uses the second
type of protein, the enzymatic protein. Again [and we could even copy and paste the
entire discussion above here], ribosomes (this time attached ribosomes) assemble AA's
into enzymatic proteins, which are made available to any part of the cell needing that
particular enzyme, or are stored in a secretory organ (for example saliva glands). Now the
instability of proteins becomes an advantage, because soon after these enzymes begin
being used, they break down into non-functional polypeptides, and whatever
reaction(s) they drive slow then stop, unless more enzyme is provided to continue the
reactions. And again, the polypeptide fragments of a former enzyme are digested to
AA's which become available for the next protein being assembled.

&nbsp &nbsp Structural proteins must be of the correct size and shape in
order to fit into the larger structure (such as a cell) being built or repaired
[something about square pegs and round holes]. Enzymatic proteins, as predicted by
the Lock and Key hypothesis, must have the correct size and shape to fit onto the
substrate and bring the active site adjacent to the bond to be formed or broken [the
key must fit the key hole, and the notches must match the tumblers inside the lock].
In a word, shape is important for the ability of a protein to serve its purpose.
Protein structure comes as primary, secondary, tertiary, and sometimes quaternary.
Primary structure is the AA sequence which is assembled by the ribosomes into a
linear [remember zig and zag] molecule. For insulin, this is 87 AA's, which make up
the primary structure of inactive insulin. Secondary structure results as the
levo-rotary zags cause the long molecule to coil around itself, and form Hydrogen
bonds [more Chemistry not found in your notes, but available from any introductory
Biology textbook]. For insulin, the secondary structure of the inactive form is
‘pretzel’-shaped (and still 87 AA's long). The tertiary shape is formed
after 36 AA's are removed from the single curve side of the pretzel (as opposed to
the double curve side), leaving a 21 AA piece and a 30 AA piece which fold on each
other and bond together into a complex, bow-tie shaped structure. This is the active
form of insulin which mediates the conversion of glucose to glycogen. If it were less
complicated, and ribosomes made the 51 AA active form, glucose would always be
converted to glycogen, leaving none in the blood stream. The entire Human species
would be dying in a diabetic coma, or would be already dead; translated to English,
we would be extinct, which we are not. For those proteins with quaternary structure,
two or more polypeptides are Hydrogen-bonded together to form a large functional
structure. To explain the importance of AA sequence to students at a College-prep
High School [and later, introductory Biology students], I came up with the following
headline:
&nbsp &nbsp “MIJORITY APPROVE PRESIDENT'S PULICY”
which has two typographical errors (one critical, one non-critical). So your
challenge is to determine whether or not the President is still popular. Starting
with the non-critical error (because you can guess what word was intended
before you correct it), the U in PULICY clearly should be an O in POLICY:
&nbsp &nbsp “MIJORITY APPROVE PRESIDENT'S
PULICY”
&nbsp &nbsp “MIJORITY APPROVE PRESIDENT'S
POLICY”
The other error is critical because there are two possible errors, and
correcting them produces opposite meanings:
either (1) the first I in MIJORITY should be an A:
&nbsp &nbsp “MIJORITY APPROVE PRESIDENT'S
POLICY”
&nbsp &nbsp “MAJORITY APPROVE PRESIDENT'S
POLICY” in which case the president is still popular,
or (2) the J in MIJORITY should be an N:
&nbsp &nbsp “MIJORITY APPROVE PRESIDENT'S
POLICY”
&nbsp &nbsp “MINORITY APPROVE PRESIDENT'S
POLICY” in which case the President is no longer popular,
[he/she was popular (or
“POP-u-lur” if you've seen Wicked) at one time, at least before the
election]. The headline as written cannot be interpreted with more than a 50-50
chance of being correct. A single ‘typo’ in a protein can be corrected [in
theory] with a 1 in 20 chance of being correct. In real living creatures, errors in
proteins are corrected by running them through the paper shredder.

§ 3. As an energy source

Protein, or more accurately, amino acids, can be used as an energy source, but in
the real world [not on MTV, but where actual, living Humans are found], this is
limited to emergency situations, such as carbohydrate starvation. Unfortunately, the
only substrate for the metabolic processes which capture energy in a useful form
(ATP's) is sugar, or anything that looks chemically like sugar. Amino acids look
nothing like sugar due to the Nitrogen-containing amino group. The amino group can be
removed by hydrolysis, by splitting a water (H-OH) into a Hydrogen (H-) and a
hydroxyl (-OH) [like separating a Nabisco Oreo (or Sunshine Hydrox cookie)
into a chocolate cookie and a chocolate cookie with cream filing on it (the Hydrox
cookie is a good mneumonic for remembering the Hydrox-yl group; the chocolate
cookies represent Hydrogen atoms, and the cream filling represents an Oxygen atom)].
These break the bond holding the amino on the amino acid, and place the Hydrogen (H-)
on the amine (-NH2) making NH3, or Ammonia. The hydroxyl (-OH)
is attached to the central Carbon of the amino acid making a deaminated amino acid
HO-(HCR)-(C=O)-OH, which then is converted [at the expense of several
ATP's] to a sugar-like substance and metabolized to yield ATP's, but net production
is less than what you would get from a perfectly good carbohydrate. The Ammonia is
highly toxic; it's the ingredient in Windex (and other cleaning products) that
is responsible for the burning sensation in your eyes and nose, [as tissue damage
begins]. The Ammonia is immediatedly converted [at an additional cost of ATP's] to
urea, which only poisonous enough to kill you (uremic poisoning). Under normal
conditions, the urea is diluted with water to make urine [a solution of urea &amp
water], and excreted through the kidneys and sweat glands, producing an unpleasant
body odor.

&nbsp &nbsp When Humans are forced into using protein as their primary
energy source due to actual (carbohydrate) starvation a number of problems
arise. [a 100 g bowl of brown rice provides about 362 Calories, so 3 bowls of rice
during a ‘good’ week barely meets the absolute minimum Calorie intake need
of 800 Cal/DAY; some starving children in developing countries do get up to
3 bowls, 300 g, of rice a week, but not always from charities that advertise on
TV]. First, the amino acid sources are damaged proteins [which are not replaced
because of a dietary deficiency of protein [brown rice provides 7 g of incomplete
protein per 100 g rice, the polished white rice seen in TV commercials for charities
provide only 6.8g (data from
FAO Food and
Nutrition Division, Food and Agriculture Organization of the United Nations,
Rome, Italy); a 100g or about 3.5 oz top sirloin steak provides 29.4g protein
(data from
highproteinfoods.net)].
To put it simply, the protein source used for energy is the Human's body!
Probably depending on genetics, the excess urea produced (beyond what can be removed
by the now poorly functioning kidneys) may be converted to uric acid, resulting in
the total body swelling (edema) associated with kwashiorkor [in mild cases, the
swelling is confined to the lower extremities and is called gout]; otherwise, the
patient develops marasmus due to loss of muscle and other tissues. Both kwashiorkor
and marasmus are fatal, unless reversed by early intervention with an aggresive
nutritionally sound diet.
&nbsp When Humans are forced into utilizing protein as their primary energy source
on purpose [this sometimes occurs in the magical fantasy world of easy weight loss
programs], (surprise, surprise!) the amino acid source used is polypeptides from
damaged protein -not dietary protein. Unneeded amino acids from digestion are
not absorbed, because amino acids are absorbed by active transport rather than the
passive (or facilitated) absorption used for sugars and fatty acids. Surplus amino
acids from digestion are used to enrich the fecal material. Since the body cannot
distinquish between actual starvation due to inadequate food supply and induced
carbohydrate starvation recommended by ‘weight management counselors,’ the
effects on the body are the same. The amino acids which are deaminated to be used for
energy capture come from the patient's muscle mass (and other organs, including vital
organs such as hearts). While the loss of muscle mass does produce weight loss, the
body fat percentage increases initially [remember, a drop in carbohydrate density in
the food intake triggers fat deposition into adipose]. Long term deliberate
starvation will eventually drive mobilization of adipose fat as a energy source, but
the damage due to amino acid utilization will not reverse [and will continue] until
the body believes that winter is over [detected by an sizable increase in
carbohydrate density of the food intake]. Back in the real world, winter usually
lasts less than 6 months (it only feels longer), so cavemen survived the Pleistocene
Ice Age, reproduced, and Homo sapiens is still here. By the way, the high
protein weight loss diets typically use the presence of ketones in the urine as an
indicator that the diet is “working” Urinary ketones is the first sign of
uremic poisoning, requiring intervention to reverse the problem, because it is
a treatable, but potentially life-threatening, medical condition.